The Belgian international was sent off in Wednesday's League Cup semi-final second leg at Swansea City after kicking the teenager while trying to get the ball as the ballboy laid on top of it. Both individuals subsequently apologised.
Hazard received an automatic three-match ban for his 78th-minute red card but could now face a longer suspension. He has until Tuesday to respond to the charge.
The game ended in a 0-0 draw, sending Swansea through to next month's Wembley final against fourth-tier Bradford City 2-0 on aggregate.
"It is alleged that Hazard's behaviour in relation to a Swansea City ballboy... constituted violent conduct whereby the standard punishment that would otherwise apply was clearly insufficient," the FA said in a statement.
Hazard has received plenty of sympathy from Premier League managers and players who have criticised 17-year-old ballboy Charlie Morgan for time-wasting.
While the FA's statement did not directly condemn Morgan, it did say it wanted to "remind all clubs of their responsibilities in ensuring ballboys and other personnel around the pitch act in an appropriate manner at all times".
Queens Park Rangers manager Harry Redknapp was among those to defend Hazard who has said he never intended to kick the ballboy and thought he had made contact with the ball rather than him.
"He hasn't kicked the boy, he toe-poked the ball under the boy's body," Redknapp told a news conference on Friday.
"Why is the kid lying on the ball in the first place? Imagine the frustration, you're the player trying to get to a cup final and there's this kid behaving like an idiot lying on the ball, won't give the ball back.
"He didn't kick the kid, he kicked the ball underneath him and I think the whole thing got blown out of all proportion. I can think of a lot of players who would have kicked a bit harder than what he kicked."
Arsenal manager Arsene Wenger had a similar view.
"Ballboys are there to get the ball quickly back to the players and into the game, they are not there to waste time," he said.
"Hazard is not a violent player, he wanted to get the ball back as quickly as possible. In my opinion he went in a little bit too strongly but I don't think he wanted to hurt the boy, he just wanted to get the ball back."
